sdsc / cipres-roll

SDSC cipres roll

SDSC "cipres" roll

Overview

This roll bundles CIPRES applications.

For more information about the bundled applications, please visit the official web pages.

• FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.

Requirements

To build/install this roll you must have root access to a Rocks development machine (e.g., a frontend or development appliance).

If your Rocks development machine does not have Internet access you must download the appropriate cipres source file(s) using a machine that does have Internet access and copy them into the src/cipres directories on your Rocks development machine.

Dependencies

The sdsc-roll must be installed on the build machine, since the build process depends on make include files provided by that roll.

The roll sources assume that modulefiles provided by SDSC compiler rolls are available, but it will build without them as long as the environment variables they provide are otherwise defined.

Building

To build the cipres-roll, execute this on a Rocks development machine (e.g., a frontend or development appliance):

% make 2>&1 | tee build.log

A successful build will create the file cipres-*.disk1.iso. If you built the roll on a Rocks frontend, proceed to the installation step. If you built the roll on a Rocks development appliance, you need to copy the roll to your Rocks frontend before continuing with installation.

This roll source supports building with different compilers. The ROLLCOMPILER make variable can be used to specify the names of compiler modulefiles to use for building the software, e.g.,

make ROLLCOMPILER=intel 2>&1 | tee build.log

The build process recognizes "gnu", "intel" or "pgi" as the value for the ROLLCOMPILER variable. The default value is "gnu".

Installation

To install, execute these instructions on a Rocks frontend:

% rocks add roll *.iso
% rocks enable roll cipres
% cd /export/rocks/install
% rocks create distro

Subsequent installs of compute and login nodes will then include the contents of the cipres-roll. To avoid cluttering the cluster frontend with unused software, the cipres-roll is configured to install only on compute and login nodes. To force installation on your frontend, run this command after adding the cipres-roll to your distro

% rocks run roll cipres host=NAME | bash

where NAME is the DNS name of a compute or login node in your cluster.

In addition to the software itself, the roll installs cipres environment module files in:

/opt/modulefiles/applications/cipres

Testing

The cipres-roll includes a test script which can be run to verify proper installation of the roll documentation, binaries and module files. To run the test scripts execute the following command(s):

% /root/rolltests/cipres.t